[Biojava-l] DBREF parsing exception...

[Andreas Prlic]

Hi Jay,

are you using the version from SVN or a particular release?

I think this is already fixed in SVN...

Andreas

On Sun, Mar 6, 2011 at 5:54 PM, Jay Vyas <jayunit100 at gmail.com> wrote:
> Hi guys : It looks like the PDB parser for biojava is tripping up on the
> DBREFs for pdb id 3O62 .  Its a little bit of a problem for me because
> a bunch of exception stack traces are getting streamed to the screen and
> making it difficult for me to debug my code....
>
> Is there a way to disable the reading of DBREF lines, or alternatively, is
> there
> a way to fix the exception ?
>
> badly formatted line ... DBREF  3O62 A    1   135  UNP    P84233
> H32_XENLA        2    136
> java.lang.StringIndexOutOfBoundsException: String index out of range: 68
>    at java.lang.String.substring(String.java:1934)
>    at
> org.biojava.bio.structure.io.PDBFileParser.pdb_DBREF_Handler(PDBFileParser.java:1979)
>    at
> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2413)
>
> --
> Jay Vyas
> MMSB/UCHC
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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